The objective of this paper is to report the effects that control/operational strategies may have on plant-wide phosphorus (P) transformations in wastewater treatment plants (WWTP). The development of a new set of biological (activated sludge, anaerobic digestion), physico-chemical (aqueous phase, precipitation, mass transfer) process models and model interfaces (between water and sludge line) were required to describe the required tri-phasic (gas, liquid, solid) compound transformations and the close interlinks between the P and the sulfur (S) and iron (Fe) cycles. A modified version of the Benchmark Simulation Model No. 2 (BSM2) (open loop) is used as test platform upon which three different operational alternatives (A1, A2, A3) are evaluated. Rigorous sensor and actuator models are also included in order to reproduce realistic control actions. Model-based analysis shows that the combination of an ammonium ( [Formula: see text] ) and total suspended solids (XTSS) control strategy (A1) better adapts the system to influent dynamics, improves phosphate [Formula: see text] accumulation by phosphorus accumulating organisms (XPAO) (41%), increases nitrification/denitrification efficiency (18%) and reduces aeration energy (Eaeration) (21%). The addition of iron ( [Formula: see text] ) for chemical P removal (A2) promotes the formation of ferric oxides (XHFO-H, XHFO-L), phosphate adsorption (XHFO-H,P, XHFO-L,P), co-precipitation (XHFO-H,P,old, XHFO-L,P,old) and consequently reduces the P levels in the effluent (from 2.8 to 0.9 g P.m-3). This also has an impact on the sludge line, with hydrogen sulfide production ( [Formula: see text] ) reduced (36%) due to iron sulfide (XFeS) precipitation. As a consequence, there is also a slightly higher energy production (Eproduction) from biogas. Lastly, the inclusion of a stripping and crystallization unit (A3) for P recovery reduces the quantity of P in the anaerobic digester supernatant returning to the water line and allows potential struvite ( [Formula: see text] ) recovery ranging from 69 to 227 kg.day-1 depending on: (1) airflow (Qstripping); and, (2) magnesium ( [Formula: see text] ) addition. All the proposed alternatives are evaluated from an environmental and economical point of view using appropriate performance indices. Finally, some deficiencies and opportunities of the proposed approach when performing (plant-wide) wastewater treatment modelling/engineering projects are discussed.